Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004161.1 Hibiscus syriacus cultivar Beakdansim tig00009102_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 77420
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:503 original size:29 final size:30
Alignment explanation
Indices: 457--514 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
447 TAAAACATAA
*
457 TATATAACATACTAATATTTATTTTCCAAAT
1 TATATAACATAATAATA-TTATTTTCCAAAT
*
488 TATATAA-ATAAT-ATATTATTTTTCAAA
1 TATATAACATAATAATATTATTTTCCAAA
515 AATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 3 0.12
30 4 0.16
31 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (30 bp):
TATATAACATAATAATATTATTTTCCAAAT
Found at i:519 original size:27 final size:27
Alignment explanation
Indices: 469--529 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
459 TATAACATAC
*
469 TAATATTTATTTTCCAAATTATATAAA
1 TAATATTTATTTTCCAAATAATATAAA
* *
496 TAATATATTATTTTTCAAA-AATATATA
1 TAATAT-TTATTTTCCAAATAATATAAA
523 T-ATATTT
1 TAATATTT
530 TAAAAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 4 0.13
27 13 0.43
28 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATATTTATTTTCCAAATAATATAAA
Found at i:520 original size:29 final size:27
Alignment explanation
Indices: 469--522 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
459 TATAACATAC
* *
469 TAATATTTATTTTCCAAATTATATAAA
1 TAATATTTATTTTCAAAAATATATAAA
496 TAATATATTATTTTTCAAAAATATATA
1 TAATAT-TTA-TTTTCAAAAATATATA
523 TATATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 3 0.13
29 14 0.61
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (27 bp):
TAATATTTATTTTCAAAAATATATAAA
Found at i:525 original size:22 final size:21
Alignment explanation
Indices: 493--547 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
483 CAAATTATAT
*
493 AAATA-ATATATTATTTTTCAA
1 AAATATATATATTA-TTTTAAA
514 AAATATATATA-TATTTTAAA
1 AAATATATATATTATTTTAAA
534 AAACTATAATATAT
1 AAA-TAT-ATATAT
548 ACTACTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 9 0.31
21 10 0.34
22 10 0.34
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATATATATTATTTTAAA
Found at i:535 original size:20 final size:20
Alignment explanation
Indices: 492--547 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
482 CCAAATTATA
*
492 TAAATAATATAT-TAT-TTT
1 TAAAAAATATATATATATTT
*
510 TCAAAAATATATATATATTT
1 TAAAAAATATATATATATTT
530 TAAAAAACTATA-ATATAT
1 TAAAAAA-TATATATATAT
548 ACTACTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 10 0.31
19 3 0.09
20 15 0.47
21 4 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAAATATATATATATTT
Found at i:548 original size:22 final size:22
Alignment explanation
Indices: 495--548 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
485 AATTATATAA
*
495 ATAATATATTATTTTTCAAAAAT
1 ATAATATA-TATTTTTAAAAAAT
518 AT-ATATATA-TTTTAAAAAACT
1 ATAATATATATTTTTAAAAAA-T
539 ATAATATATA
1 ATAATATATA
549 CTACTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 9 0.32
21 5 0.18
22 12 0.43
23 2 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATATATATTTTTAAAAAAT
Found at i:1238 original size:129 final size:128
Alignment explanation
Indices: 1074--1454 Score: 299
Period size: 128 Copynumber: 3.0 Consensus size: 128
1064 CAGGAAAAAG
* *
1074 TTGATTCACTTCACTGCTCTTCAGGGAAGACTGAATCAGGGTAGATTTGATCCACTGCTCTTCAG
1 TTGATTCACTTCACTGCTCTTCAGGAAAGACTGAATCAGGGTAGATTTGATCCACTACTCTTCAG
*** * * *
1139 AGAAAATCAAATCTAGAAATGGGATCTGCTTCACTACTCTTTAGGGAAGATCATATC-TG-AAAC
66 AGAAAATCAAATCTAGAAA-AAAATATACTTCA-TACTCTTTAGGGAAGATCAGA-CATGTAAAC
1202 T
128 T
** * * * * * * *
1203 TTGATTCACTTCTTTGCTCCTT-AGGAAAGATTGAATTAGTGTTGATTTGCTTCATTACTCTTCA
1 TTGATTCACTTCACTGCT-CTTCAGGAAAGACTGAATCAGGGTAGATTTGATCCACTACTCTTCA
* * * *
1267 GGGAAGATCAAATCTAGAAAAAAATATACTTCATACTCTTTAGTGAAGATTAGACATGTAAACT
65 GAGAAAATCAAATCTAGAAAAAAATATACTTCATACTCTTTAGGGAAGATCAGACATGTAAACT
** * * * * *
1331 TTGATTCACTTCACTAATCTTTAAGG-AAGA-TATAATC-GAGGTTGATTTGCTTCACTACTCTT
1 TTGATTCACTTCACTGCTC-TTCAGGAAAGACT-GAATCAG-GGTAGATTTGATCCACTACTCTT
* * * * * * * *
1393 TAGTGAAGATCGAATCTGGAAAAGGAGATATGCTTCGCTACTCTTTA-GGAAGATCAGACATG
63 CAGAGAAAATCAAATCTAGAAAA--AAATATACTTC-ATACTCTTTAGGGAAGATCAGACATG
1455 CAAATCAAAT
Statistics
Matches: 204, Mismatches: 38, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
126 1 0.00
127 23 0.11
128 76 0.37
129 70 0.34
130 25 0.12
131 9 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (128 bp):
TTGATTCACTTCACTGCTCTTCAGGAAAGACTGAATCAGGGTAGATTTGATCCACTACTCTTCAG
AGAAAATCAAATCTAGAAAAAAATATACTTCATACTCTTTAGGGAAGATCAGACATGTAAACT
Found at i:6678 original size:17 final size:17
Alignment explanation
Indices: 6634--6678 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
6624 CACCTTTATA
* *
6634 TCATGATGATATAGATG
1 TCATGAGGATGTAGATG
6651 TCATGAGGATGTAGATG
1 TCATGAGGATGTAGATG
6668 TCATGAGGATG
1 TCATGAGGATG
6679 CAAAAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (17 bp):
TCATGAGGATGTAGATG
Found at i:8265 original size:15 final size:12
Alignment explanation
Indices: 8233--8284 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
8223 TAAAATACTA
8233 ATAATAATTAAT
1 ATAATAATTAAT
8245 ATAATAATTAAT
1 ATAATAATTAAT
* *
8257 GATTAAATAAATAAA
1 -A-T-AATAATTAAT
8272 ATAATAAATTAAT
1 ATAAT-AATTAAT
8285 TAACCTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 15 0.47
13 7 0.22
14 2 0.06
15 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
ATAATAATTAAT
Found at i:9941 original size:6 final size:6
Alignment explanation
Indices: 9930--10008 Score: 59
Period size: 6 Copynumber: 13.2 Consensus size: 6
9920 GCGAATTTTA
* * * * * * * *
9930 TCTTGC TCTTGC TTTTAC ACTTGT TATTGC TTTTGC TCTTGT TCTTTC
1 TCTTGC TCTTGC TCTTGC TCTTGC TCTTGC TCTTGC TCTTGC TCTTGC
* * *
9978 TCTTGT TATTGC TCTTGT TCTTGC TCTTGC T
1 TCTTGC TCTTGC TCTTGC TCTTGC TCTTGC T
10009 TCACTACTCT
Statistics
Matches: 52, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.05, C:0.23, G:0.14, T:0.58
Consensus pattern (6 bp):
TCTTGC
Found at i:9966 original size:30 final size:31
Alignment explanation
Indices: 9930--10002 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
9920 GCGAATTTTA
9930 TCTTGCTCTTGCTT-TTACACTTGTTATTGC
1 TCTTGCTCTTGCTTCTTACACTTGTTATTGC
* * *
9960 TTTTGCTCTTG-TTCTTTCTCTTGTTATTGC
1 TCTTGCTCTTGCTTCTTACACTTGTTATTGC
*
9990 TCTTGTTCTTGCT
1 TCTTGCTCTTGCT
10003 CTTGCTTCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.06
30 33 0.92
31 1 0.03
ACGTcount: A:0.05, C:0.22, G:0.14, T:0.59
Consensus pattern (31 bp):
TCTTGCTCTTGCTTCTTACACTTGTTATTGC
Found at i:9982 original size:12 final size:12
Alignment explanation
Indices: 9962--10006 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
9952 GTTATTGCTT
9962 TTGCTCTTGTTC
1 TTGCTCTTGTTC
* *
9974 TTTCTCTTGTTA
1 TTGCTCTTGTTC
9986 TTGCTCTTGTTC
1 TTGCTCTTGTTC
9998 TTGCTCTTG
1 TTGCTCTTG
10007 CTTCACTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.02, C:0.22, G:0.16, T:0.60
Consensus pattern (12 bp):
TTGCTCTTGTTC
Found at i:13690 original size:13 final size:14
Alignment explanation
Indices: 13656--13685 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
13646 TTGAATTACC
13656 TTTCCTTT-TTCTT
1 TTTCCTTTCTTCTT
13669 TTTCCTTTCTTCTT
1 TTTCCTTTCTTCTT
13683 TTT
1 TTT
13686 GTTTCATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCCTTTCTTCTT
Found at i:15755 original size:15 final size:16
Alignment explanation
Indices: 15731--15769 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
15721 GCTTCAATTG
*
15731 ATGCTCTTACCAT-AA
1 ATGCTTTTACCATAAA
15746 ATGCTTTTACCATAAA
1 ATGCTTTTACCATAAA
15762 ATGCTTTT
1 ATGCTTTT
15770 GGTACCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (16 bp):
ATGCTTTTACCATAAA
Found at i:18329 original size:19 final size:20
Alignment explanation
Indices: 18305--18347 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
18295 GGCTTTATGA
18305 ATAATA-ATA-ATAATATTAT
1 ATAATATATAGATAATA-TAT
18324 ATAATATATATGATAATATAT
1 ATAATATATA-GATAATATAT
18345 ATA
1 ATA
18348 GTAAAACGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 6 0.29
22 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAATATATAGATAATATAT
Found at i:18345 original size:12 final size:11
Alignment explanation
Indices: 18305--18347 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
18295 GGCTTTATGA
18305 ATAATA-ATA-
1 ATAATATATAT
18314 ATAATAT-TAT
1 ATAATATATAT
18324 ATAATATATAT
1 ATAATATATAT
18335 GATAATATATAT
1 -ATAATATATAT
18347 A
1 A
18348 GTAAAACGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.27
10 7 0.23
11 4 0.13
12 11 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
ATAATATATAT
Found at i:20218 original size:23 final size:23
Alignment explanation
Indices: 20192--20269 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
20182 GACCACACTG
*
20192 GTGGCTTTGAGTGAGCCATACAC
1 GTGGCTTTGAGTGAGCCATACGC
* *
20215 GTGGTTTTGAGTGAGCCATACGT
1 GTGGCTTTGAGTGAGCCATACGC
*
20238 GTGGCTTTGAGTGAGCCGTACGC
1 GTGGCTTTGAGTGAGCCATACGC
20261 GTGGCTTTG
1 GTGGCTTTG
20270 GAAGTAGTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.15, C:0.18, G:0.36, T:0.31
Consensus pattern (23 bp):
GTGGCTTTGAGTGAGCCATACGC
Found at i:24444 original size:24 final size:24
Alignment explanation
Indices: 24299--24434 Score: 218
Period size: 24 Copynumber: 5.7 Consensus size: 24
24289 TTCTATTATA
* *
24299 ATACCTGACTTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
24323 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
24347 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
24371 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* * * *
24395 ATATTTGACCTGGATTTTGACCTG
1 ATACTTGACCTGGATTCTGATCGG
24419 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
24435 ATGTTTTGAT
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 105 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:24649 original size:2 final size:2
Alignment explanation
Indices: 24642--24670 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24632 TGGATGGGGG
24642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24671 GTTTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25421 original size:17 final size:17
Alignment explanation
Indices: 25378--25423 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
25368 CGGGTCGGGT
*
25378 ATATATATATATATTTA
1 ATATATATATATAATTA
* *
25395 AAATAAATATATAATTA
1 ATATATATATATAATTA
*
25412 TTATATATATAT
1 ATATATATATAT
25424 TTTTAATTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATAATTA
Found at i:25422 original size:34 final size:34
Alignment explanation
Indices: 25379--25461 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
25369 GGGTCGGGTA
25379 TATATATATATATTTAAAATAAATATATAA-TTAT
1 TATATATATATATTTAAAATAAATATA-AATTTAT
* ** *
25413 TATATATATATTTTTAATTTAAATTTAAATTTAT
1 TATATATATATATTTAAAATAAATATAAATTTAT
25447 TAATATTATATATAT
1 T-ATA-TATATATAT
25462 ATATATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 2 0.05
34 28 0.68
35 3 0.07
36 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
TATATATATATATTTAAAATAAATATAAATTTAT
Found at i:25442 original size:40 final size:38
Alignment explanation
Indices: 25377--25468 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 38
25367 TCGGGTCGGG
25377 TATATATATATATATTTAAAATAAATATA-TAATTATTA
1 TATATATATATATATTTAAAATAAATATATTAA-TATTA
* * * *
25415 TATATATATTTTTAATTTAAATTTAAATTTATTAATATTA
1 TATATATATATAT-ATTTAAA-ATAAATATATTAATATTA
25455 TATATATATATATA
1 TATATATATATATA
25469 ATAATTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 11 0.24
39 8 0.18
40 23 0.51
41 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TATATATATATATATTTAAAATAAATATATTAATATTA
Found at i:25482 original size:42 final size:41
Alignment explanation
Indices: 25377--25489 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 41
25367 TCGGGTCGGG
* *
25377 TATATATATATAT-ATTTAAA-ATAA-ATATA-TAATTATTA
1 TATATATATATATAATTTAAATTTAATATTTATTAA-TATTA
* *
25415 TATATATATTTTTAATTTAAATTTAA-ATTTATTAATATTA
1 TATATATATATATAATTTAAATTTAATATTTATTAATATTA
**
25455 TATATATATATATAATAATTATTTTTAATATTTAT
1 TATATATATATATAAT--TTAAATTTAATATTTAT
25490 CGGGTTGGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 11 0.18
39 7 0.11
40 26 0.43
41 3 0.05
42 8 0.13
43 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
TATATATATATATAATTTAAATTTAATATTTATTAATATTA
Found at i:26288 original size:40 final size:40
Alignment explanation
Indices: 26224--26358 Score: 191
Period size: 40 Copynumber: 3.4 Consensus size: 40
26214 TGAGTCAAAT
* *
26224 ATATGCACCGTAGTAC-TTACACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCACC
* *
26263 ATATGCACCAAAGTGCATTACACATAAGGTCGTGTCCACC
1 ATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCACC
* * * *
26303 ATATGCACTGAAGTGCATTACAGATAAGGTCGCGCCTACC
1 ATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCACC
26343 ATATGCACCGAAGTGC
1 ATATGCACCGAAGTGC
26359 TTAATCGATA
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 13 0.15
40 71 0.85
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (40 bp):
ATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCACC
Found at i:29840 original size:17 final size:17
Alignment explanation
Indices: 29820--29870 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
29810 GAAAGTCAAC
*
29820 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCA
29837 GGTCAACGGTCGGGTCA
1 GGTCAACGGTCGGGTCA
*
29854 GGTCAACAGTCGGGTCA
1 GGTCAACGGTCGGGTCA
29871 ACAGTCGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.18, C:0.24, G:0.41, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCA
Found at i:29865 original size:29 final size:29
Alignment explanation
Indices: 29833--29889 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
29823 CAACGGTCGG
*
29833 GTCGGGTCAACGGTCGGGTCAGGTCAACA
1 GTCGGGTCAACAGTCGGGTCAGGTCAACA
*
29862 GTCGGGTCAACAGTCGGGTCGGGTCAAC
1 GTCGGGTCAACAGTCGGGTCAGGTCAAC
29890 CCGGTTCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.18
Consensus pattern (29 bp):
GTCGGGTCAACAGTCGGGTCAGGTCAACA
Found at i:29869 original size:12 final size:12
Alignment explanation
Indices: 29854--29881 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29844 GGTCGGGTCA
29854 GGTCAACAGTCG
1 GGTCAACAGTCG
29866 GGTCAACAGTCG
1 GGTCAACAGTCG
29878 GGTC
1 GGTC
29882 GGGTCAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.25, G:0.36, T:0.18
Consensus pattern (12 bp):
GGTCAACAGTCG
Found at i:29882 original size:17 final size:17
Alignment explanation
Indices: 29820--29889 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
29810 GAAAGTCAAC
*
29820 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
* *
29837 GGTCAACGGTCGGGTCA
1 GGTCAACAGTCGGGTCG
29854 GGTCAACA-----GTCG
1 GGTCAACAGTCGGGTCG
29866 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
29883 GGTCAAC
1 GGTCAAC
29890 CCGGTTCAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 11 0.24
17 34 0.76
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:29907 original size:19 final size:19
Alignment explanation
Indices: 29883--29952 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
29873 AGTCGGGTCG
* *
29883 GGTCAACCCGGTTCAGATC
1 GGTCAAACCGGTTCAGACC
*
29902 GGTCAAACCGGTTCGGACC
1 GGTCAAACCGGTTCAGACC
* *
29921 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
29941 GGTCAAACCGGT
1 GGTCAAACCGGT
29953 GGAAAATTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 30 0.68
20 14 0.32
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:29936 original size:10 final size:10
Alignment explanation
Indices: 29885--29952 Score: 52
Period size: 9 Copynumber: 7.0 Consensus size: 10
29875 TCGGGTCGGG
*
29885 TCAACCCGGT
1 TCAAACCGGT
* *
29895 TCAGATCGG-
1 TCAAACCGGT
29904 TCAAACCGGT
1 TCAAACCGGT
**
29914 TCGGACCGG-
1 TCAAACCGGT
29923 TCAAACCGGT
1 TCAAACCGGT
*
29933 TCAAAACTGG-
1 TC-AAACCGGT
29943 TCAAACCGGT
1 TCAAACCGGT
29953 GGAAAATTCC
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
9 20 0.47
10 17 0.40
11 6 0.14
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:29958 original size:20 final size:20
Alignment explanation
Indices: 29921--29958 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29911 GGTTCGGACC
*
29921 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTGCAAAACT
*
29941 GGTCAAACCGGTGGAAAA
1 GGTCAAACCGGTGCAAAA
29959 TTCCCGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (20 bp):
GGTCAAACCGGTGCAAAACT
Found at i:37090 original size:13 final size:13
Alignment explanation
Indices: 37072--37121 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
37062 AAGAAAGTCA
37072 ACGGTCAACGGTC
1 ACGGTCAACGGTC
37085 ACGGTCAACGGTC
1 ACGGTCAACGGTC
37098 AACGGTC-A-GGTC
1 -ACGGTCAACGGTC
*
37110 -GGGTCAACGGTC
1 ACGGTCAACGGTC
37122 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
10 4 0.12
11 1 0.03
12 8 0.24
13 14 0.42
14 6 0.18
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.16
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:37093 original size:20 final size:19
Alignment explanation
Indices: 37068--37126 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 19
37058 GTCAAAGAAA
37068 GTCAACGGTCAACGGTCACG
1 GTCAACGGTCAACGGTCA-G
37088 GTCAACGGTCAACGGTCAG
1 GTCAACGGTCAACGGTCAG
* *
37107 GTC--GGGTCAACGGTCGG
1 GTCAACGGTCAACGGTCAG
37124 GTC
1 GTC
37127 GGGTCAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 15 0.41
19 4 0.11
20 18 0.49
ACGTcount: A:0.20, C:0.27, G:0.36, T:0.17
Consensus pattern (19 bp):
GTCAACGGTCAACGGTCAG
Found at i:37116 original size:17 final size:17
Alignment explanation
Indices: 37094--37168 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
37084 CACGGTCAAC
*
37094 GGTCAACGGTCAGGTCG
1 GGTCAACGGTCGGGTCG
37111 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
37128 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
37145 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
37162 GGTCAAC
1 GGTCAAC
37169 CCGGTTCAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:37121 original size:7 final size:7
Alignment explanation
Indices: 37068--37105 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
37058 GTCAAAGAAA
37068 GTCAACG
1 GTCAACG
37075 GTCAACG
1 GTCAACG
37082 GTC-ACG
1 GTCAACG
37088 GTCAACG
1 GTCAACG
37095 GTCAACG
1 GTCAACG
37102 GTCA
1 GTCA
37106 GGTCGGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:42540 original size:40 final size:40
Alignment explanation
Indices: 42494--42608 Score: 187
Period size: 40 Copynumber: 2.9 Consensus size: 40
42484 ATCGTAGTGT
42494 TTACACATAAGTTCGTGCCCACCATATGCACCGAAGTGCA
1 TTACACATAAGTTCGTGCCCACCATATGCACCGAAGTGCA
* *
42534 TTACACATAAGGTCATGCCCACCATATGCACCGAAGTGCA
1 TTACACATAAGTTCGTGCCCACCATATGCACCGAAGTGCA
*
42574 TTACACATAAGGTT-GTGCCCACCATATGCAACGAA
1 TTACACATAA-GTTCGTGCCCACCATATGCACCGAA
42609 ATGCTTAATC
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
40 67 0.97
41 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (40 bp):
TTACACATAAGTTCGTGCCCACCATATGCACCGAAGTGCA
Found at i:44075 original size:29 final size:30
Alignment explanation
Indices: 44016--44082 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
44006 AAACAATCCA
* * * * *
44016 TAACTTTCCCAAAATTATCGATTTGTCCCC
1 TAACTTTTCAAAAATTATAGAATGGTCCCC
44046 TAACTTTTCAAAAATTATAGAATGGT-CCC
1 TAACTTTTCAAAAATTATAGAATGGTCCCC
*
44075 TAAATTTT
1 TAACTTTT
44083 TATAAGGCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (30 bp):
TAACTTTTCAAAAATTATAGAATGGTCCCC
Found at i:45369 original size:2 final size:2
Alignment explanation
Indices: 45358--45386 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45348 TTTATATTAA
45358 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45387 CCATTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:45493 original size:23 final size:24
Alignment explanation
Indices: 45467--45515 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
45457 ATAGGTAATA
45467 TATTTTCAAAAA-TATAT-ATATGC
1 TATTTT-AAAAATTATATAATATGC
45490 TATTTTAAAAATTATATAATATGC
1 TATTTTAAAAATTATATAATATGC
45514 TA
1 TA
45516 CTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.21
23 11 0.46
24 8 0.33
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (24 bp):
TATTTTAAAAATTATATAATATGC
Found at i:45830 original size:14 final size:14
Alignment explanation
Indices: 45811--45837 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45801 TTGATTGCTG
45811 AAAAATATTTTTTA
1 AAAAATATTTTTTA
45825 AAAAATATTTTTT
1 AAAAATATTTTTT
45838 CGATGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAAAATATTTTTTA
Found at i:46171 original size:22 final size:22
Alignment explanation
Indices: 46146--46199 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
46136 AATATTATAT
46146 TAATATATACTCATATATATTA-
1 TAATATATACTCAT-TATATTAG
* *
46168 TAATAATATATTTATTATATTAG
1 TAAT-ATATACTCATTATATTAG
46191 TAATATATA
1 TAATATATA
46200 ATACGTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATATATACTCATTATATTAG
Found at i:46178 original size:17 final size:17
Alignment explanation
Indices: 46104--46186 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 17
46094 TTTAACAAAC
*
46104 ATATAGTATAATTTTAATA
1 ATATA-TAT-ATTATAATA
*
46123 ATAT-TATATT-T-TTA
1 ATATATATATTATAATA
46137 ATAT-TATATTAATATATA
1 ATATATATATT-ATA-ATA
*
46155 CTCATATATATTATAATA
1 AT-ATATATATTATAATA
*
46173 ATATATTTATTATA
1 ATATATATATTATA
46187 TTAGTAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
14 12 0.23
15 1 0.02
16 4 0.08
17 14 0.26
18 7 0.13
19 9 0.17
20 6 0.11
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
ATATATATATTATAATA
Found at i:53228 original size:14 final size:15
Alignment explanation
Indices: 53209--53242 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
53199 GTGGATGCAA
53209 ACAAGAAAAGC-TAT
1 ACAAGAAAAGCGTAT
*
53223 ACAAGAAAGGCGTAT
1 ACAAGAAAAGCGTAT
53238 ACAAG
1 ACAAG
53243 CAATCTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.53, C:0.15, G:0.21, T:0.12
Consensus pattern (15 bp):
ACAAGAAAAGCGTAT
Found at i:54791 original size:27 final size:27
Alignment explanation
Indices: 54751--54807 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
54741 TTTTAGAATC
* *
54751 TTTTATATTTTAATTT-TTTTTATATT
1 TTTTATATTATAATTTATTTTCATATT
*
54777 TTTTATATTAATAATTTATTTTCATCTT
1 TTTTATATT-ATAATTTATTTTCATATT
54805 TTT
1 TTT
54808 AAAACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 9 0.35
27 6 0.23
28 11 0.42
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTATATTATAATTTATTTTCATATT
Found at i:54806 original size:26 final size:26
Alignment explanation
Indices: 54748--54806 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
54738 AATTTTTAGA
* * *
54748 ATCTTTTATATTTTAATTTTTTTTAT
1 ATCTTTTATATTATAATTTATTTTAC
*
54774 ATTTTTTATATTAATAATTTATTTT-C
1 ATCTTTTATATT-ATAATTTATTTTAC
54800 ATCTTTT
1 ATCTTTT
54807 TAAAACTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (26 bp):
ATCTTTTATATTATAATTTATTTTAC
Found at i:54808 original size:27 final size:26
Alignment explanation
Indices: 54751--54808 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
54741 TTTTAGAATC
* * *
54751 TTTTATATTTTAATTTTTTTTATATT
1 TTTTATATTATAATTTTTTTCATACT
54777 TTTTATATTAATAATTTATTTTCAT-CT
1 TTTTATATT-ATAATTT-TTTTCATACT
54804 TTTTA
1 TTTTA
54809 AAACTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 12 0.44
28 6 0.22
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTATATTATAATTTTTTTCATACT
Found at i:56213 original size:21 final size:21
Alignment explanation
Indices: 56165--56223 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
56155 GTCCGAGTTA
*
56165 CCCGCGATGGCCACAATAGCG
1 CCCGCGATGGCCGCAATAGCG
* * *
56186 TCTGCGATGGCCGCAATAGTG
1 CCCGCGATGGCCGCAATAGCG
**
56207 CCCGCGACAGCCGCAAT
1 CCCGCGATGGCCGCAAT
56224 CACGGTAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.36, G:0.29, T:0.14
Consensus pattern (21 bp):
CCCGCGATGGCCGCAATAGCG
Found at i:57043 original size:19 final size:19
Alignment explanation
Indices: 57019--57061 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
57009 CACATCATAG
* *
57019 ATATAGTTTTTTAAAAAAT
1 ATATAGGTTTTGAAAAAAT
*
57038 ATATAGGTTTTGAAAATAT
1 ATATAGGTTTTGAAAAAAT
57057 ATATA
1 ATATA
57062 ATATATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (19 bp):
ATATAGGTTTTGAAAAAAT
Found at i:57068 original size:45 final size:46
Alignment explanation
Indices: 56990--57125 Score: 127
Period size: 45 Copynumber: 2.9 Consensus size: 46
56980 GCATACATAT
* * * *
56990 AATATATAGTTTTTGAAAACACATCAT-AGATATAGTTTTTT-AAAA
1 AATATATAGGTTTTGAAAATATAT-ATAATATATAGTTTTTTGAAAA
57035 AATATATAGGTTTTGAAAATATATATAATATATA-TAATTTTTGAAAA
1 AATATATAGGTTTTGAAAATATATATAATATATAGT--TTTTTGAAAA
*
57082 CATATTATA-GTTTATGAAAATATAATATATATTATATAGTTTTT
1 AATA-TATAGGTTT-TGAAAATAT-ATATA-A-TATATAGTTTTT
57126 AAGGAATATA
Statistics
Matches: 76, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
44 3 0.04
45 27 0.36
46 5 0.07
47 11 0.14
48 13 0.17
49 5 0.07
50 5 0.07
51 6 0.08
52 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (46 bp):
AATATATAGGTTTTGAAAATATATATAATATATAGTTTTTTGAAAA
Found at i:57076 original size:47 final size:49
Alignment explanation
Indices: 57019--57125 Score: 141
Period size: 47 Copynumber: 2.2 Consensus size: 49
57009 CACATCATAG
*
57019 ATATAGTTTTTTAAAAAATA-TATAGGTTT-TGAAAATAT-ATATA-ATAT
1 ATATAGTTTTTGAAAAAATATTATA-GTTTATGAAAATATAATATATAT-T
* *
57066 ATATAATTTTTGAAAACATATTATAGTTTATGAAAATATAATATATATT
1 ATATAGTTTTTGAAAAAATATTATAGTTTATGAAAATATAATATATATT
57115 ATATAGTTTTT
1 ATATAGTTTTT
57126 AAGGAATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
47 21 0.40
48 13 0.25
49 16 0.31
50 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (49 bp):
ATATAGTTTTTGAAAAAATATTATAGTTTATGAAAATATAATATATATT
Found at i:57099 original size:20 final size:21
Alignment explanation
Indices: 57062--57112 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
57052 AATATATATA
*
57062 ATATATATAATTTTTGAAAAC
1 ATATATATAATTTATGAAAAC
* *
57083 ATAT-TATAGTTTATGAAAAT
1 ATATATATAATTTATGAAAAC
57103 ATAATATATA
1 AT-ATATATA
57113 TTATATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 15 0.60
21 6 0.24
22 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
ATATATATAATTTATGAAAAC
Found at i:57154 original size:3 final size:3
Alignment explanation
Indices: 57146--57173 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
57136 TGCATATACA
57146 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
57174 TCTCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:60156 original size:20 final size:18
Alignment explanation
Indices: 60131--60170 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
60121 CTAACTTATT
*
60131 TTCTTTTGTTTATTTCTTTA
1 TTCTTTT-TTTACTT-TTTA
60151 TTCTTTTTTTACTTTTTA
1 TTCTTTTTTTACTTTTTA
60169 TT
1 TT
60171 GATTGTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (18 bp):
TTCTTTTTTTACTTTTTA
Found at i:65341 original size:19 final size:19
Alignment explanation
Indices: 65317--65357 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
65307 TAGTTAAAGT
65317 TTTCAGGCCAGG-CATCAAC
1 TTTCAGGCCAGGTC-TCAAC
65336 TTTCAGGCCAGGTCTCAAC
1 TTTCAGGCCAGGTCTCAAC
65355 TTT
1 TTT
65358 ATGACGGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (19 bp):
TTTCAGGCCAGGTCTCAAC
Found at i:66300 original size:28 final size:30
Alignment explanation
Indices: 66265--66330 Score: 95
Period size: 28 Copynumber: 2.3 Consensus size: 30
66255 TTATATATGG
*
66265 CATA-TATAGA-ATATATAGTTTTTGAAAA
1 CATATTATAGACATATATAATTTTTGAAAA
66293 CAT-TTATA-ACATATATAATTTTTGAAAA
1 CATATTATAGACATATATAATTTTTGAAAA
66321 CATATTATAG
1 CATATTATAG
66331 TTTTTGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.03
28 27 0.82
29 5 0.15
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (30 bp):
CATATTATAGACATATATAATTTTTGAAAA
Found at i:66356 original size:24 final size:24
Alignment explanation
Indices: 66275--66374 Score: 100
Period size: 24 Copynumber: 4.2 Consensus size: 24
66265 CATATATAGA
* *
66275 ATATATAGTTTTTGAAAACATTTATAAC
1 ATATATAGTTTTTG-AAA-A-TAAT-AT
* *
66303 ATATATAATTTTTG--AA-AACAT
1 ATATATAGTTTTTGAAAATAATAT
66324 AT-TATAGTTTTTGAAAATAATAT
1 ATATATAGTTTTTGAAAATAATAT
66347 ATATATAGTTTTTGAAAATAATAT
1 ATATATAGTTTTTGAAAATAATAT
66371 ATAT
1 ATAT
66375 TATATAGTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
20 10 0.16
21 3 0.05
22 3 0.05
23 6 0.10
24 26 0.42
25 1 0.02
28 13 0.21
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (24 bp):
ATATATAGTTTTTGAAAATAATAT
Found at i:66369 original size:27 final size:23
Alignment explanation
Indices: 66275--66403 Score: 93
Period size: 24 Copynumber: 5.3 Consensus size: 23
66265 CATATATAGA
*
66275 ATATATAGTTTTTGAAAACATTTATAAC
1 ATATATAGTTTTTG-AAA-A--TAT-AT
* *
66303 ATATATAATTTTTG-AAA-ACAT
1 ATATATAGTTTTTGAAAATATAT
66324 AT-TATAGTTTTTGAAAATAATAT
1 ATATATAGTTTTTGAAAAT-ATAT
66347 ATATATAGTTTTTGAAAATAATATAT
1 ATATATAGTTTTTG--AA-AATATAT
*
66373 ATTATATAGTTTTTAATAAATATAT
1 A-TATATAGTTTTTGA-AAATATAT
*
66398 ACATAT
1 ATATAT
66404 TATTATTATT
Statistics
Matches: 85, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
20 10 0.12
21 6 0.07
22 1 0.01
23 5 0.06
24 15 0.18
25 10 0.12
26 10 0.12
27 15 0.18
28 13 0.15
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (23 bp):
ATATATAGTTTTTGAAAATATAT
Found at i:66372 original size:20 final size:20
Alignment explanation
Indices: 66303--66373 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
66293 CATTTATAAC
* *
66303 ATATATAATTTTTGAAAA-C
1 ATATATAGTTTTTGAAAATA
66322 ATATTATAGTTTTTGAAAATAATA
1 ATA-TATAGTTTTTG--AA-AATA
66346 TATATATAGTTTTTGAAAATA
1 -ATATATAGTTTTTGAAAATA
66367 ATATATA
1 ATATATA
66374 TTATATAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 17 0.39
21 4 0.09
22 4 0.09
23 2 0.05
24 11 0.25
25 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATATAGTTTTTGAAAATA
Found at i:66403 original size:29 final size:27
Alignment explanation
Indices: 66326--66406 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 27
66316 GAAAACATAT
*
66326 TATAGTTTTTGAAAATAAT--ATA-TA
1 TATAGTTTTTAAAAATAATACATATTA
* *
66350 TATAGTTTTTGAAAATAATATATATTA
1 TATAGTTTTTAAAAATAATACATATTA
66377 TATAGTTTTTAATAAATATATACATATTA
1 TATAGTTTTTAA-AAATA-ATACATATTA
66406 T
1 T
66407 TATTATTTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
24 19 0.38
26 3 0.06
27 13 0.26
28 5 0.10
29 10 0.20
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (27 bp):
TATAGTTTTTAAAAATAATACATATTA
Found at i:66432 original size:7 final size:7
Alignment explanation
Indices: 66414--66463 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
66404 TATTATTATT
66414 TCTTTT-
1 TCTTTTC
66420 TCTTTTC
1 TCTTTTC
66427 TCTTTTC
1 TCTTTTC
66434 TCTTTTC
1 TCTTTTC
66441 TC-TTT-
1 TCTTTTC
66446 TCTTTT-
1 TCTTTTC
66452 T-TTTTC
1 TCTTTTC
66458 TCTTTT
1 TCTTTT
66464 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 6 0.15
6 14 0.35
7 20 0.50
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TCTTTTC
Found at i:66439 original size:14 final size:13
Alignment explanation
Indices: 66414--66463 Score: 61
Period size: 12 Copynumber: 3.9 Consensus size: 13
66404 TATTATTATT
66414 TCTTTTTCTTTTC
1 TCTTTTTCTTTTC
66427 TCTTTTCTCTTTTC
1 TCTTTT-TCTTTTC
66441 TC-TTTTCTTTT-
1 TCTTTTTCTTTTC
66452 T-TTTTCTCTTTT
1 TCTTTT-TCTTTT
66464 TTTTTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.12
12 12 0.35
13 9 0.26
14 9 0.26
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTTTTCTTTTC
Found at i:66478 original size:15 final size:18
Alignment explanation
Indices: 66459--66504 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
66449 TTTTTTTTCT
66459 CTTTT-TTTTTATT-TTA
1 CTTTTATTTTTATTATTA
66475 -TTTTATTTATTATTATTA
1 CTTTTATTT-TTATTATTA
66493 CTTTTATTTTTA
1 CTTTTATTTTTA
66505 GGTTTGATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.15
16 3 0.12
17 5 0.19
18 6 0.23
19 8 0.31
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTTATTTTTATTATTA
Found at i:67880 original size:17 final size:19
Alignment explanation
Indices: 67855--67893 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
67845 TTTAATACAA
67855 TTTAGTCTTGATT-TTTAT
1 TTTAGTCTTGATTATTTAT
*
67873 TTTA-TCTTGTTTATTTAT
1 TTTAGTCTTGATTATTTAT
67891 TTT
1 TTT
67894 CTTTCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTAGTCTTGATTATTTAT
Found at i:72717 original size:17 final size:17
Alignment explanation
Indices: 72682--72729 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
72672 GAAACTTGTC
72682 AATTATTTTATAAAA-TAA
1 AATTA-TTTA-AAAATTAA
72700 AATTATTTAAAAATTAA
1 AATTATTTAAAAATTAA
72717 AATT-TTTAAAAAT
1 AATTATTTAAAAAT
72730 AATTAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.45
17 11 0.38
18 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATTTAAAAATTAA
Found at i:73336 original size:16 final size:16
Alignment explanation
Indices: 73312--73346 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
73302 GATGACTAAA
* *
73312 TTTATTTTAATTTATT
1 TTTAATTTAATATATT
73328 TTTAATTTAATATATT
1 TTTAATTTAATATATT
73344 TTT
1 TTT
73347 GGGTAAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTTAATATATT
Found at i:73560 original size:31 final size:31
Alignment explanation
Indices: 73522--73589 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
73512 CCCTAAGTCG
73522 AGGGACTAAAATCAAATGGATCGATAATATT
1 AGGGACTAAAATCAAATGGATCGATAATATT
*
73553 AGGGACTAAAATCAAATGGATCGATAATGTT
1 AGGGACTAAAATCAAATGGATCGATAATATT
73584 AGGGAC
1 AGGGAC
73590 CATTCCCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (31 bp):
AGGGACTAAAATCAAATGGATCGATAATATT
Found at i:73881 original size:19 final size:18
Alignment explanation
Indices: 73830--73882 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
73820 ATATTTATAT
* *
73830 ATCTTAACATAAATTCAC
1 ATCTTAACATAATTTTAC
*
73848 ATATTAA-ACTAATTTTAC
1 ATCTTAACA-TAATTTTAC
73866 ATCTTAACATTAATTTT
1 ATCTTAACA-TAATTTT
73883 TTTTATCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 1 0.04
18 19 0.68
19 8 0.29
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (18 bp):
ATCTTAACATAATTTTAC
Found at i:74064 original size:27 final size:26
Alignment explanation
Indices: 74031--74138 Score: 87
Period size: 26 Copynumber: 4.0 Consensus size: 26
74021 TTTTATTATG
*
74031 ATAATATCTTAAATTTAAGATAAAAAT
1 ATAATATTTTAAA-TTAAGATAAAAAT
* *
74058 ATAATATATTTTTTTAGTTAAGATAAAAAT
1 AT-A-ATA--TTTTAAATTAAGATAAAAAT
*
74088 AT-ATATTTTATAATTAAAATAAAAAT
1 ATAATATTTTA-AATTAAGATAAAAAT
* *
74114 AT-AT-TTTTAAGTTAAGATAATAAT
1 ATAATATTTTAAATTAAGATAAAAAT
74138 A
1 A
74139 AAAGATATGT
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
24 13 0.19
25 9 0.13
26 17 0.25
27 5 0.07
28 1 0.01
29 3 0.04
30 15 0.22
31 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.43
Consensus pattern (26 bp):
ATAATATTTTAAATTAAGATAAAAAT
Found at i:74115 original size:24 final size:23
Alignment explanation
Indices: 74063--74138 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 23
74053 AAAATATAAT
* *
74063 ATATTTTTTTAGTTAAGATAAAAA
1 ATATATTTTTAATTAAGAT-AAAA
*
74087 TATATATTTTATAATTAAAATAAAA
1 -ATATATTTT-TAATTAAGATAAAA
*
74112 ATATATTTTTAAGTTAAGATAATA
1 ATATATTTTTAA-TTAAGATAAAA
74136 ATA
1 ATA
74139 AAAGATATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.07
24 21 0.48
25 12 0.27
26 8 0.18
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
ATATATTTTTAATTAAGATAAAA
Found at i:74139 original size:30 final size:29
Alignment explanation
Indices: 74045--74361 Score: 148
Period size: 30 Copynumber: 11.2 Consensus size: 29
74035 TATCTTAAAT
* * *
74045 TTAAGATAAAAATATAATATATTTTTTTAG
1 TTAAGATAATAATAAAATATA-TTTTTAAG
*
74075 TTAAGAT-A-AA-AATATATATTTTATAA-
1 TTAAGATAATAATAAAATATATTTT-TAAG
74101 TT-A-A-AAT-A-AAAATATATTTTTAAG
1 TTAAGATAATAATAAAATATATTTTTAAG
*
74125 TTAAGATAATAATAAAAGATATGTTTTAAG
1 TTAAGATAATAATAAAATATAT-TTTTAAG
* * ** * ** *
74155 TTAAAAT-AGAATTTATTATATTAATAAT
1 TTAAGATAATAATAAAATATATTTTTAAG
* * *
74183 TTAAGGTAATAATAGAATATATTTAATAA-
1 TTAAGATAATAATAAAATATATTT-TTAAG
* * * * **
74212 TTCAAGTTAATAATATAATTTCTGTAATAAG
1 TT-AAGATAATAATAAAATATAT-TTTTAAG
*
74243 TTAAGATGAGT-ATAAAATATA-TTTTAAG
1 TTAAGAT-AATAATAAAATATATTTTTAAG
* * * *
74271 TTAAAATAAGAATAAACTATATTTTTAGG
1 TTAAGATAATAATAAAATATATTTTTAAG
* **
74300 TTAAGA-AGA-GATAAAATAT-TTAATAAG
1 TTAAGATA-ATAATAAAATATATTTTTAAG
*
74327 TT-A-ATAAAAATAAAATATATTTTTAATG
1 TTAAGATAATAATAAAATATATTTTTAA-G
74355 TTAAGAT
1 TTAAGAT
74362 GTAAAATTAA
Statistics
Matches: 215, Mismatches: 47, Indels: 50
0.69 0.15 0.16
Matches are distributed among these distances:
23 3 0.01
24 16 0.07
25 4 0.02
26 18 0.08
27 24 0.11
28 44 0.20
29 44 0.20
30 57 0.27
31 5 0.02
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (29 bp):
TTAAGATAATAATAAAATATATTTTTAAG
Found at i:74270 original size:28 final size:29
Alignment explanation
Indices: 74239--74362 Score: 114
Period size: 28 Copynumber: 4.4 Consensus size: 29
74229 ATTTCTGTAA
*
74239 TAAGTTAAGATGAGTATAAAATATA-TTT
1 TAAGTTAAGATGAGAATAAAATATATTTT
* * *
74267 TAAGTTAAAATAAGAATAAACTATATTTT
1 TAAGTTAAGATGAGAATAAAATATATTTT
* * **
74296 TAGGTTAAGAAGAG-ATAAAATAT-TTAA
1 TAAGTTAAGATGAGAATAAAATATATTTT
* *
74323 TAAGTT-A-ATAAAAATAAAATATATTTT
1 TAAGTTAAGATGAGAATAAAATATATTTT
74350 TAATGTTAAGATG
1 TAA-GTTAAGATG
74363 TAAAATTAAT
Statistics
Matches: 72, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
25 2 0.03
26 10 0.14
27 12 0.17
28 32 0.44
29 14 0.19
30 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (29 bp):
TAAGTTAAGATGAGAATAAAATATATTTT
Found at i:74340 original size:54 final size:57
Alignment explanation
Indices: 74242--74360 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 57
74232 TCTGTAATAA
* * * *
74242 GTTAAGATGAGTATAAAATATATTTTAAGTTAAAATAAGAATAAACTATATTTTT-AG
1 GTTAAGAAGAGTATAAAATATATTATAAGTT-AAATAAAAATAAAATATATTTTTAAG
*
74299 GTTAAGAAGAG-ATAAAATAT-TTAATAAGTT-AATAAAAATAAAATATATTTTTAAT
1 GTTAAGAAGAGTATAAAATATATT-ATAAGTTAAATAAAAATAAAATATATTTTTAAG
74354 GTTAAGA
1 GTTAAGA
74361 TGTAAAATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
54 20 0.36
55 10 0.18
56 15 0.27
57 10 0.18
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (57 bp):
GTTAAGAAGAGTATAAAATATATTATAAGTTAAATAAAAATAAAATATATTTTTAAG
Found at i:74389 original size:18 final size:19
Alignment explanation
Indices: 74348--74389 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
74338 AAAATATATT
74348 TTTAATGTTAAGATGTAAA
1 TTTAATGTTAAGATGTAAA
* * *
74367 ATTAAT-TTAATATGTGAA
1 TTTAATGTTAAGATGTAAA
74385 TTTAA
1 TTTAA
74390 GCTAAGATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (19 bp):
TTTAATGTTAAGATGTAAA
Found at i:75199 original size:2 final size:2
Alignment explanation
Indices: 75192--75236 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
75182 AGAATGTTTG
75192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75234 AT A
1 AT A
75237 GAGAGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75241 original size:2 final size:2
Alignment explanation
Indices: 75236--75262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
75226 ATATATATAT
75236 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
75263 TTGAAAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.